Add test for DMSReader convert_pos_from_native with non-zero unit cell - #5307
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…step Closes MDAnalysis#5127. The elif branch in DumpReader._read_next_timestep that raises ValueError when a specific coordinate convention is requested but not present in the file had no test coverage. Add test_missing_convention_in_timestep which uses LAMMPSDUMP (scaled coords only) with lammps_coordinate_convention="unscaled" to trigger the error.
The existing test only uses a DMS file with all-zero cell vectors, so ts.dimensions ends up None and the convert_pos_from_native branch for dimensions was never exercised. Add TestDMSReaderWithBox which builds a minimal DMS SQLite file in tmp_path with a real orthorhombic box and checks that dimensions are read and not None. Closes MDAnalysis#3304 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## develop #5307 +/- ##
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+ Coverage 93.82% 93.84% +0.01%
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Files 182 182
Lines 22487 22487
Branches 3196 3196
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+ Hits 21099 21102 +3
+ Misses 925 923 -2
+ Partials 463 462 -1 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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Summary
Closes #3304.
The existing
TestDMSReaderonly loadsadk_closed.dms, which has all-zero global_cell vectors.triclinic_boxconverts those to a zero array,Timestep.dimensionssetter treats that asNone, so the branch atDMS.py:115(if self.ts.dimensions is not None: convert_pos_from_native(ts.dimensions[:3])) was never reached by any test.This PR adds
TestDMSReaderWithBoxwhich:tmp_pathwith a real 30x40x50 Angstrom orthorhombic boxts.dimensions is not NoneTest plan
python -m pytest testsuite/MDAnalysisTests/coordinates/test_dms.py -v— 12 passedpython -m pytest testsuite/MDAnalysisTests/topology/test_dms.py -v— 22 passed🤖 Generated with Claude Code
📚 Documentation preview 📚: https://mdanalysis--5307.org.readthedocs.build/en/5307/